The best of both worlds: Combining lineage-specific and
universal bait sets in target-enrichment hybridization
reactions

J 2021

The best of both worlds: Combining lineage-specific and universal bait sets in target-enrichment hybridization reactions

HENDRIKS, K.P., Terezie MALÍK MANDÁKOVÁ, N.M. HAY, E. LY, A.H. VAN HUYSDUYNEN et. al.

Základní údaje

Originální název

The best of both worlds: Combining lineage-specific and universal bait sets in target-enrichment hybridization reactions

Autoři

HENDRIKS, K.P., Terezie MALÍK MANDÁKOVÁ (203 Česká republika, domácí), N.M. HAY, E. LY, A.H. VAN HUYSDUYNEN, R. TAMRAKAR, S.K. THOMAS, O. TORO-NUNEZ, J.C. PIRES, L.A. NIKOLOV, M.A. KOCH, M.D. WINDHAM, Martin LYSÁK (203 Česká republika, garant, domácí), F. FOREST, K. MUMMENHOFF, W.J. BAKER, F. LENS a C.D. BAILEY

Vydání

Applications in Plant Sciences, HOBOKEN, Wiley, 2021, 2168-0450

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10611 Plant sciences, botany

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 2.511

Kód RIV

RIV/00216224:14740/21:00119664

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1002/aps3.11438

UT WoS

000670213700001

Klíčová slova anglicky

Brassicaceae; combining probes; enrichment; Hyb-Seq; phylogenomics; phylogeny; population biology; target enrichment

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 21. 2. 2022 21:42, Mgr. Pavla Foltynová, Ph.D.

Anotace

V originále

Premise Researchers adopting target-enrichment approaches often struggle with the decision of whether to use universal or lineage-specific probe sets. To circumvent this quandary, we investigate the efficacy of a simultaneous enrichment by combining universal probes and lineage-specific probes in a single hybridization reaction, to benefit from the qualities of both probe sets with little added cost or effort. Methods and Results Using 26 Brassicaceae libraries and standard enrichment protocols, we compare results from three independent data sets. A large average fraction of reads mapping to the Angiosperms353 (24-31%) and Brassicaceae (35-59%) targets resulted in a sizable reconstruction of loci for each target set (x >= 70%). Conclusions High levels of enrichment and locus reconstruction for the two target sets demonstrate that the sampling of genomic regions can be easily extended through the combination of probe sets in single enrichment reactions. We hope that these findings will facilitate the production of expanded data sets that answer individual research questions and simultaneously allow wider applications by the research community as a whole.

Návaznosti

GA21-06839S, projekt VaV

Název: Vznik a evoluce chromozomů spojených s apomixií v rodu Boechera (Brassicaceae)

Investor: Grantová agentura ČR, The origin and evolution of apomixis-related chromosomes in Boechera (Brassicaceae)

LTAUSA17002, projekt VaV

Název: Role hybridizace a apomixie v evoluci tribu Boechereae

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Role hybridizace a apomixie v evoluci tribu Boechereae, INTER-ACTION

Citovat

HENDRIKS, K.P., Terezie MALÍK MANDÁKOVÁ, N.M. HAY, E. LY, A.H. VAN HUYSDUYNEN, R. TAMRAKAR, S.K. THOMAS, O. TORO-NUNEZ, J.C. PIRES, L.A. NIKOLOV, M.A. KOCH, M.D. WINDHAM, Martin LYSÁK, F. FOREST, K. MUMMENHOFF, W.J. BAKER, F. LENS a C.D. BAILEY. The best of both worlds: Combining lineage-specific and universal bait sets in target-enrichment hybridization reactions. Applications in Plant Sciences. HOBOKEN: Wiley, 2021, roč. 9, č. 7, s. „e11438“, 12 s. ISSN 2168-0450. Dostupné z: https://dx.doi.org/10.1002/aps3.11438.

@article{1836117,
   author = {Hendriks, K.P. and Malík Mandáková, Terezie and Hay, N.M. and Ly, E. and van Huysduynen, A.H. and Tamrakar, R. and Thomas, S.K. and ToroandNunez, O. and Pires, J.C. and Nikolov, L.A. and Koch, M.A. and Windham, M.D. and Lysák, Martin and Forest, F. and Mummenhoff, K. and Baker, W.J. and Lens, F. and Bailey, C.D.},
   article_location = {HOBOKEN},
   article_number = {7},
   doi = {http://dx.doi.org/10.1002/aps3.11438},
   keywords = {Brassicaceae; combining probes; enrichment; Hyb-Seq; phylogenomics; phylogeny; population biology; target enrichment},
   language = {eng},
   issn = {2168-0450},
   journal = {Applications in Plant Sciences},
   title = {The best of both worlds: Combining lineage-specific and universal bait sets in target-enrichment hybridization reactions},
   url = {https://bsapubs.onlinelibrary.wiley.com/doi/10.1002/aps3.11438},
   volume = {9},
   year = {2021}
}

TY  - JOUR
ID  - 1836117
AU  - Hendriks, K.P. - Malík Mandáková, Terezie - Hay, N.M. - Ly, E. - van Huysduynen, A.H. - Tamrakar, R. - Thomas, S.K. - Toro-Nunez, O. - Pires, J.C. - Nikolov, L.A. - Koch, M.A. - Windham, M.D. - Lysák, Martin - Forest, F. - Mummenhoff, K. - Baker, W.J. - Lens, F. - Bailey, C.D.
PY  - 2021
TI  - The best of both worlds: Combining lineage-specific and universal bait sets in target-enrichment hybridization reactions
JF  - Applications in Plant Sciences
VL  - 9
IS  - 7
SP  - „e11438“
EP  - „e11438“
PB  - Wiley
SN  - 21680450
KW  - Brassicaceae
KW  - combining probes
KW  - enrichment
KW  - Hyb-Seq
KW  - phylogenomics
KW  - phylogeny
KW  - population biology
KW  - target enrichment
UR  - https://bsapubs.onlinelibrary.wiley.com/doi/10.1002/aps3.11438
N2  - Premise Researchers adopting target-enrichment approaches often struggle with the decision of whether to use universal or lineage-specific probe sets. To circumvent this quandary, we investigate the efficacy of a simultaneous enrichment by combining universal probes and lineage-specific probes in a single hybridization reaction, to benefit from the qualities of both probe sets with little added cost or effort. Methods and Results Using 26 Brassicaceae libraries and standard enrichment protocols, we compare results from three independent data sets. A large average fraction of reads mapping to the Angiosperms353 (24-31%) and Brassicaceae (35-59%) targets resulted in a sizable reconstruction of loci for each target set (x >= 70%). Conclusions High levels of enrichment and locus reconstruction for the two target sets demonstrate that the sampling of genomic regions can be easily extended through the combination of probe sets in single enrichment reactions. We hope that these findings will facilitate the production of expanded data sets that answer individual research questions and simultaneously allow wider applications by the research community as a whole.
ER  -

HENDRIKS, K.P., Terezie MALÍK MANDÁKOVÁ, N.M. HAY, E. LY, A.H. VAN HUYSDUYNEN, R. TAMRAKAR, S.K. THOMAS, O. TORO-NUNEZ, J.C. PIRES, L.A. NIKOLOV, M.A. KOCH, M.D. WINDHAM, Martin LYSÁK, F. FOREST, K. MUMMENHOFF, W.J. BAKER, F. LENS a C.D. BAILEY. The best of both worlds: Combining lineage-specific and universal bait sets in target-enrichment hybridization reactions. \textit{Applications in Plant Sciences}. HOBOKEN: Wiley, 2021, roč.~9, č.~7, s.~„e11438“, 12 s. ISSN~2168-0450. Dostupné z: https://dx.doi.org/10.1002/aps3.11438.

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